This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 6 Casal2 model configurations (3 BetaDiff and 3 ADOL-C).
The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-6 vs. 2e-3).
The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-6 vs. 2e-3).
The main characteristics of the Test Case LIN (ling) CASAL model are:
Observation data include:
Parameters estimated include:
## [1] "Tue Aug 31 12:48:49 2021"
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 11 (bullseye)
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
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## locale:
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## [5] LC_MONETARY=en_NZ.UTF-8 LC_MESSAGES=en_NZ.UTF-8
## [7] LC_PAPER=en_NZ.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] Casal2_21.08 casal_2.30 devtools_2.4.2 usethis_2.0.1 rlist_0.4.6.1
## [6] ggthemes_4.2.4 gridExtra_2.3 coda_0.19-4 ggmcmc_1.5.1.1 ggplot2_3.3.5
## [11] tidyr_1.1.3 dplyr_1.0.7
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## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.7 lattice_0.20-41 prettyunits_1.1.1 ps_1.6.0
## [5] assertthat_0.2.1 rprojroot_2.0.2 digest_0.6.27 utf8_1.2.2
## [9] R6_2.5.1 plyr_1.8.6 evaluate_0.14 pillar_1.6.2
## [13] rlang_0.4.11 rstudioapi_0.13 data.table_1.14.0 callr_3.7.0
## [17] jquerylib_0.1.4 rmarkdown_2.10 desc_1.3.0 stringr_1.4.0
## [21] munsell_0.5.0 compiler_3.6.3 xfun_0.25 pkgconfig_2.0.3
## [25] pkgbuild_1.2.0 htmltools_0.5.2 tidyselect_1.1.1 tibble_3.1.4
## [29] reshape_0.8.8 fansi_0.5.0 crayon_1.4.1 withr_2.4.2
## [33] grid_3.6.3 jsonlite_1.7.2 GGally_2.1.2 gtable_0.3.0
## [37] lifecycle_1.0.0 DBI_1.1.1 magrittr_2.0.1 scales_1.1.1
## [41] cli_3.0.1 stringi_1.7.4 cachem_1.0.6 remotes_2.4.0
## [45] fs_1.5.0 testthat_3.0.4 bslib_0.2.5.1 ellipsis_0.3.2
## [49] generics_0.1.0 vctrs_0.3.8 RColorBrewer_1.1-2 tools_3.6.3
## [53] glue_1.4.2 purrr_0.3.4 processx_3.5.2 pkgload_1.2.1
## [57] fastmap_1.1.0 yaml_2.2.1 colorspace_2.0-2 sessioninfo_1.1.1
## [61] memoise_2.0.0 knitr_1.33 sass_0.4.0
source('../../R-functions/report_read_in_CASAL_MPD_files.R')
source('../../R-functions/report_read_in_Casal2_MPD_files.R')
Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results
| rownames | Base_Model | Sensitivity_1 | Percent_Diff |
|---|---|---|---|
| q[tan_sum].q | 0.09128 | 0.09105 | 0.252 |
| q[tan_aut].q | 0.12620 | 0.12590 | 0.238 |
| initialization.B0 | 309000.00000 | 310700.00000 | -0.550 |
| natural_mortality.ogive_all1 | 12.49000 | 12.98000 | -3.923 |
| natural_mortality.ogive_all2 | 0.13270 | 0.12780 | 3.693 |
| natural_mortality.ogive_all3 | 0.38190 | 0.44990 | -17.806 |
| natural_mortality.ogive_all4 | 0.35060 | 0.35390 | -0.941 |
| selectivity[surveysum_sel].male1 | 4.73800 | 4.88100 | -3.018 |
| selectivity[surveysum_sel].male2 | 1.75000 | 1.77200 | -1.257 |
| selectivity[surveysum_sel].male3 | 0.61000 | 0.60160 | 1.377 |
| selectivity[surveysum_sel].female1 | 5.46000 | 5.61300 | -2.802 |
| selectivity[surveysum_sel].female2 | 2.20600 | 2.21500 | -0.408 |
| selectivity[surveyaut_sel].male1 | 5.50400 | 5.64400 | -2.544 |
| selectivity[surveyaut_sel].male2 | 2.31400 | 2.29800 | 0.691 |
| selectivity[surveyaut_sel].male3 | 0.93920 | 0.93310 | 0.649 |
| selectivity[surveyaut_sel].female1 | 5.92000 | 6.06200 | -2.399 |
| selectivity[surveyaut_sel].female2 | 2.77800 | 2.73800 | 1.440 |
| selectivity[trawl_sel].male1 | 8.37000 | 8.40400 | -0.406 |
| selectivity[trawl_sel].male2 | 1.97200 | 1.94700 | 1.268 |
| selectivity[trawl_sel].male3 | 61.65000 | 200.00000 | -224.412 |
| selectivity[trawl_sel].male4 | 1.04100 | 1.02100 | 1.921 |
| selectivity[trawl_sel].female1 | 8.66400 | 8.74100 | -0.889 |
| selectivity[trawl_sel].female2 | 2.10000 | 2.08800 | 0.571 |
| selectivity[trawl_sel].female3 | 43.31000 | 40.38000 | 6.765 |
| selectivity[line_home_sel].male1 | 11.45000 | 8.58300 | 25.039 |
| selectivity[line_home_sel].male2 | 8.59000 | 4.54700 | 47.066 |
| selectivity[line_home_sel].male3 | 0.38010 | 0.26910 | 29.203 |
| selectivity[line_home_sel].female1 | 9.61600 | 9.53100 | 0.884 |
| selectivity[line_home_sel].female2 | 3.87500 | 3.68500 | 4.903 |
| selectivity[line_spawn_sel].male1 | 18.30000 | 14.04000 | 23.279 |
| selectivity[line_spawn_sel].male2 | 13.67000 | 10.01000 | 26.774 |
| selectivity[line_spawn_sel].male3 | 1.86800 | 1.17300 | 37.206 |
| selectivity[line_spawn_sel].female1 | 9.74600 | 9.71300 | 0.339 |
| selectivity[line_spawn_sel].female2 | 3.00800 | 2.89400 | 3.790 |
| recruitment.YCS1 | 1.00000 | 1.00000 | 0.000 |
| recruitment.YCS2 | 1.00000 | 1.00000 | 0.000 |
| recruitment.YCS3 | 1.00000 | 1.00000 | 0.000 |
| recruitment.YCS4 | 1.00000 | 1.00000 | 0.000 |
| recruitment.YCS5 | 0.48500 | 0.46620 | 3.876 |
| recruitment.YCS6 | 0.45830 | 0.45010 | 1.789 |
| recruitment.YCS7 | 0.56860 | 0.56470 | 0.686 |
| recruitment.YCS8 | 0.56670 | 0.56670 | 0.000 |
| recruitment.YCS9 | 0.48610 | 0.49070 | -0.946 |
| recruitment.YCS10 | 0.55500 | 0.56720 | -2.198 |
| recruitment.YCS11 | 0.56320 | 0.57880 | -2.770 |
| recruitment.YCS12 | 0.68760 | 0.71090 | -3.389 |
| recruitment.YCS13 | 0.62030 | 0.63610 | -2.547 |
| recruitment.YCS14 | 0.79060 | 0.80840 | -2.251 |
| recruitment.YCS15 | 0.46430 | 0.46930 | -1.077 |
| recruitment.YCS16 | 0.70080 | 0.70730 | -0.928 |
| recruitment.YCS17 | 0.41010 | 0.41050 | -0.098 |
| recruitment.YCS18 | 0.51500 | 0.51450 | 0.097 |
| recruitment.YCS19 | 0.34160 | 0.34220 | -0.176 |
| recruitment.YCS20 | 0.34830 | 0.34730 | 0.287 |
| recruitment.YCS21 | 0.43610 | 0.43820 | -0.482 |
| recruitment.YCS22 | 0.48060 | 0.47500 | 1.165 |
| recruitment.YCS23 | 0.45220 | 0.45130 | 0.199 |
| recruitment.YCS24 | 0.49170 | 0.49480 | -0.630 |
| recruitment.YCS25 | 0.46910 | 0.47070 | -0.341 |
| recruitment.YCS26 | 0.79930 | 0.80490 | -0.701 |
| recruitment.YCS27 | 0.79010 | 0.79210 | -0.253 |
| recruitment.YCS28 | 0.82610 | 0.83110 | -0.605 |
| recruitment.YCS29 | 0.70760 | 0.71250 | -0.692 |
| recruitment.YCS30 | 0.55170 | 0.55430 | -0.471 |
| recruitment.YCS31 | 0.47520 | 0.47680 | -0.337 |
| recruitment.YCS32 | 0.46170 | 0.46140 | 0.065 |
| recruitment.YCS33 | 0.55500 | 0.55430 | 0.126 |
| recruitment.YCS34 | 0.54670 | 0.54210 | 0.841 |
| recruitment.YCS35 | 0.48320 | 0.48250 | 0.145 |
| recruitment.YCS36 | 0.55020 | 0.54990 | 0.055 |
| recruitment.YCS37 | 0.61530 | 0.61580 | -0.081 |
| recruitment.YCS38 | 0.77570 | 0.77470 | 0.129 |
| recruitment.YCS39 | 0.63110 | 0.63060 | 0.079 |
| recruitment.YCS40 | 0.77550 | 0.77350 | 0.258 |
| recruitment.YCS41 | 0.64290 | 0.63930 | 0.560 |
| recruitment.YCS42 | 0.70670 | 0.69940 | 1.033 |
| recruitment.YCS43 | 0.65430 | 0.64860 | 0.871 |
| recruitment.YCS44 | 0.51000 | 0.50620 | 0.745 |
| recruitment.YCS45 | 0.58620 | 0.58730 | -0.188 |
| recruitment.YCS46 | 0.60350 | 0.58930 | 2.353 |
| recruitment.YCS47 | 0.57680 | 0.57450 | 0.399 |
| rownames | betadiff_casal_flags_on | betadiff_casal_flags_off | betadiff_casal_flags_on_low_tol | adolc_casal_flags_on | adolc_casal_flags_off | adolc_casal_flags_on_low_tol |
|---|---|---|---|---|---|---|
| process[Recruitment].b0 | 308529.00000 | 308529.00000 | 310577.00000 | 266100.00000 | 266100.00000 | 292654.00000 |
| catchability[summerTANq].q | 0.09137 | 0.09137 | 0.09106 | 0.10650 | 0.10650 | 0.09747 |
| catchability[autumnTANq].q | 0.12607 | 0.12607 | 0.12594 | 0.14712 | 0.14712 | 0.13444 |
| selectivity[M_all].x0 | 12.49650 | 12.49650 | 12.98440 | 14.44070 | 14.44070 | 13.00000 |
| selectivity[M_all].y0 | 0.13262 | 0.13262 | 0.12797 | 0.12992 | 0.12992 | 0.12855 |
| selectivity[M_all].y1 | 0.38280 | 0.38280 | 0.44726 | 0.28861 | 0.28861 | 0.35795 |
| selectivity[M_all].y2 | 0.35113 | 0.35113 | 0.35373 | 0.39560 | 0.39560 | 0.36956 |
| selectivity[summerTANSel_m].a50 | 4.73988 | 4.73988 | 4.87645 | 4.57732 | 4.57732 | 4.69873 |
| selectivity[summerTANSel_m].ato95 | 1.74459 | 1.74459 | 1.77029 | 1.73764 | 1.73764 | 1.74362 |
| selectivity[summerTANSel_m].alpha | 0.60995 | 0.60995 | 0.60184 | 0.61814 | 0.61814 | 0.61059 |
| selectivity[summerTANSel_f].a50 | 5.46111 | 5.46111 | 5.60807 | 5.28798 | 5.28798 | 5.42487 |
| selectivity[summerTANSel_f].ato95 | 2.20340 | 2.20340 | 2.21420 | 2.19028 | 2.19028 | 2.21398 |
| selectivity[autumnTANSel_m].a50 | 5.50982 | 5.50982 | 5.63972 | 5.73059 | 5.73059 | 5.49015 |
| selectivity[autumnTANSel_m].ato95 | 2.31271 | 2.31271 | 2.29781 | 2.99008 | 2.99008 | 2.34468 |
| selectivity[autumnTANSel_m].alpha | 0.94173 | 0.94173 | 0.93320 | 0.96024 | 0.96024 | 0.93567 |
| selectivity[autumnTANSel_f].a50 | 5.91574 | 5.91574 | 6.05848 | 5.92344 | 5.92344 | 5.91564 |
| selectivity[autumnTANSel_f].ato95 | 2.77020 | 2.77020 | 2.73846 | 3.02529 | 3.02529 | 2.83473 |
| selectivity[trwlFSel_m].mu | 8.36919 | 8.36919 | 8.40239 | 8.04058 | 8.04058 | 8.31968 |
| selectivity[trwlFSel_m].sigma_l | 1.97023 | 1.97023 | 1.94735 | 1.83023 | 1.83023 | 1.96278 |
| selectivity[trwlFSel_m].sigma_r | 61.52290 | 61.52290 | 200.00000 | 173.12600 | 173.12600 | 195.82200 |
| selectivity[trwlFSel_m].alpha | 1.04276 | 1.04276 | 1.02085 | 1.03254 | 1.03254 | 1.03107 |
| selectivity[trwlFSel_f].mu | 8.65854 | 8.65854 | 8.73949 | 8.44894 | 8.44895 | 8.64021 |
| selectivity[trwlFSel_f].sigma_l | 2.09656 | 2.09656 | 2.08849 | 2.02288 | 2.02288 | 2.10291 |
| selectivity[trwlFSel_f].sigma_r | 43.16390 | 43.16390 | 40.59470 | 74.44980 | 74.44950 | 196.08500 |
| selectivity[lineHomeFSel_m].a50 | 11.45600 | 11.45600 | 8.60835 | 11.14980 | 11.14970 | 10.33100 |
| selectivity[lineHomeFSel_m].ato95 | 8.59958 | 8.59958 | 4.59169 | 8.60490 | 8.60487 | 7.36215 |
| selectivity[lineHomeFSel_m].alpha | 0.38022 | 0.38022 | 0.26993 | 0.36159 | 0.36159 | 0.33090 |
| selectivity[lineHomeFSel_f].a50 | 9.61476 | 9.61476 | 9.53352 | 9.65872 | 9.65871 | 9.61305 |
| selectivity[lineHomeFSel_f].ato95 | 3.87014 | 3.87014 | 3.69064 | 3.95871 | 3.95871 | 3.89494 |
| selectivity[lineSpawnFSel_m].a50 | 18.21510 | 18.21510 | 14.04670 | 28.70470 | 28.70470 | 29.95770 |
| selectivity[lineSpawnFSel_m].ato95 | 13.59950 | 13.59950 | 10.02610 | 19.71220 | 19.71220 | 20.36400 |
| selectivity[lineSpawnFSel_m].alpha | 1.85634 | 1.85634 | 1.17449 | 4.70245 | 4.70245 | 4.98330 |
| selectivity[lineSpawnFSel_f].a50 | 9.73862 | 9.73862 | 9.71478 | 9.73149 | 9.73149 | 9.82125 |
| selectivity[lineSpawnFSel_f].ato95 | 2.99387 | 2.99387 | 2.89670 | 2.94900 | 2.94900 | 3.10917 |
| process[Recruitment].ycs_values{1972} | 0.48379 | 0.48379 | 0.46642 | 0.96089 | 0.96089 | 0.47028 |
| process[Recruitment].ycs_values{1973} | 0.46122 | 0.46122 | 0.45020 | 0.17029 | 0.17029 | 0.44943 |
| process[Recruitment].ycs_values{1974} | 0.56837 | 0.56837 | 0.56454 | 1.33842 | 1.33843 | 0.55135 |
| process[Recruitment].ycs_values{1975} | 0.56652 | 0.56652 | 0.56688 | 1.06126 | 1.06126 | 0.56278 |
| process[Recruitment].ycs_values{1976} | 0.48635 | 0.48635 | 0.49081 | 0.65452 | 0.65452 | 0.47857 |
| process[Recruitment].ycs_values{1977} | 0.55413 | 0.55413 | 0.56717 | 1.11613 | 1.11613 | 0.55411 |
| process[Recruitment].ycs_values{1978} | 0.56316 | 0.56316 | 0.57855 | 0.87968 | 0.87968 | 0.56121 |
| process[Recruitment].ycs_values{1979} | 0.68899 | 0.68899 | 0.71094 | 1.25909 | 1.25909 | 0.69474 |
| process[Recruitment].ycs_values{1980} | 0.62093 | 0.62093 | 0.63619 | 0.97826 | 0.97826 | 0.62242 |
| process[Recruitment].ycs_values{1981} | 0.79247 | 0.79247 | 0.80802 | 1.39968 | 1.39968 | 0.79761 |
| process[Recruitment].ycs_values{1982} | 0.46507 | 0.46507 | 0.46928 | 0.81405 | 0.81405 | 0.46578 |
| process[Recruitment].ycs_values{1983} | 0.69967 | 0.69967 | 0.70706 | 1.21889 | 1.21889 | 0.70914 |
| process[Recruitment].ycs_values{1984} | 0.40995 | 0.40995 | 0.41042 | 0.67843 | 0.67843 | 0.41357 |
| process[Recruitment].ycs_values{1985} | 0.51540 | 0.51540 | 0.51456 | 0.89968 | 0.89968 | 0.52216 |
| process[Recruitment].ycs_values{1986} | 0.34131 | 0.34131 | 0.34212 | 0.63379 | 0.63379 | 0.34658 |
| process[Recruitment].ycs_values{1987} | 0.34760 | 0.34760 | 0.34728 | 0.63848 | 0.63848 | 0.35081 |
| process[Recruitment].ycs_values{1988} | 0.43791 | 0.43791 | 0.43826 | 0.69906 | 0.69906 | 0.44356 |
| process[Recruitment].ycs_values{1989} | 0.47924 | 0.47924 | 0.47500 | 0.84529 | 0.84529 | 0.48296 |
| process[Recruitment].ycs_values{1990} | 0.45181 | 0.45181 | 0.45133 | 0.83046 | 0.83046 | 0.45748 |
| process[Recruitment].ycs_values{1991} | 0.49264 | 0.49264 | 0.49479 | 0.83278 | 0.83278 | 0.49530 |
| process[Recruitment].ycs_values{1992} | 0.46918 | 0.46918 | 0.47070 | 0.84190 | 0.84190 | 0.47280 |
| process[Recruitment].ycs_values{1993} | 0.79791 | 0.79791 | 0.80486 | 1.37198 | 1.37198 | 0.79546 |
| process[Recruitment].ycs_values{1994} | 0.79128 | 0.79128 | 0.79208 | 1.36560 | 1.36560 | 0.79353 |
| process[Recruitment].ycs_values{1995} | 0.82538 | 0.82538 | 0.83109 | 1.33636 | 1.33636 | 0.82230 |
| process[Recruitment].ycs_values{1996} | 0.70728 | 0.70728 | 0.71248 | 1.17799 | 1.17799 | 0.70676 |
| process[Recruitment].ycs_values{1997} | 0.55206 | 0.55206 | 0.55427 | 0.92843 | 0.92843 | 0.54976 |
| process[Recruitment].ycs_values{1998} | 0.47508 | 0.47508 | 0.47683 | 0.81100 | 0.81100 | 0.47576 |
| process[Recruitment].ycs_values{1999} | 0.46119 | 0.46119 | 0.46140 | 0.81281 | 0.81281 | 0.45950 |
| process[Recruitment].ycs_values{2000} | 0.55575 | 0.55575 | 0.55442 | 0.90770 | 0.90770 | 0.55642 |
| process[Recruitment].ycs_values{2001} | 0.54546 | 0.54546 | 0.54206 | 0.89998 | 0.89998 | 0.54587 |
| process[Recruitment].ycs_values{2002} | 0.48373 | 0.48373 | 0.48263 | 0.83336 | 0.83336 | 0.48578 |
| process[Recruitment].ycs_values{2003} | 0.54989 | 0.54989 | 0.54993 | 0.90389 | 0.90389 | 0.55113 |
| process[Recruitment].ycs_values{2004} | 0.61418 | 0.61418 | 0.61578 | 1.02665 | 1.02665 | 0.62023 |
| process[Recruitment].ycs_values{2005} | 0.77712 | 0.77712 | 0.77462 | 1.26528 | 1.26528 | 0.78192 |
| process[Recruitment].ycs_values{2006} | 0.63130 | 0.63130 | 0.63052 | 1.06897 | 1.06897 | 0.63677 |
| process[Recruitment].ycs_values{2007} | 0.77377 | 0.77377 | 0.77345 | 1.19541 | 1.19541 | 0.77965 |
| process[Recruitment].ycs_values{2008} | 0.64251 | 0.64251 | 0.63928 | 1.03558 | 1.03558 | 0.64725 |
| process[Recruitment].ycs_values{2009} | 0.70649 | 0.70649 | 0.69935 | 1.05005 | 1.05005 | 0.70700 |
| process[Recruitment].ycs_values{2010} | 0.65312 | 0.65312 | 0.64871 | 0.98732 | 0.98732 | 0.65008 |
| process[Recruitment].ycs_values{2011} | 0.51136 | 0.51136 | 0.50623 | 0.91803 | 0.91803 | 0.51091 |
| process[Recruitment].ycs_values{2012} | 0.58556 | 0.58556 | 0.58738 | 0.95384 | 0.95384 | 0.58606 |
| process[Recruitment].ycs_values{2013} | 0.60064 | 0.60064 | 0.58912 | 0.96522 | 0.96522 | 0.60398 |
| process[Recruitment].ycs_values{2014} | 0.57601 | 0.57601 | 0.57450 | 0.96646 | 0.96646 | 0.57961 |
| rownames | betadiff_casal_flags_on | betadiff_casal_flags_off | betadiff_casal_flags_on_low_tol | adolc_casal_flags_on | adolc_casal_flags_off | adolc_casal_flags_on_low_tol |
|---|---|---|---|---|---|---|
| process[Recruitment].b0 | 0.000 | 0.000 | -0.664 | 13.752 | 13.752 | 5.145 |
| catchability[summerTANq].q | 0.000 | 0.000 | 0.344 | -16.560 | -16.560 | -6.675 |
| catchability[autumnTANq].q | 0.000 | 0.000 | 0.105 | -16.694 | -16.694 | -6.634 |
| selectivity[M_all].x0 | 0.000 | 0.000 | -3.904 | -15.558 | -15.558 | -4.029 |
| selectivity[M_all].y0 | 0.000 | 0.000 | 3.510 | 2.041 | 2.041 | 3.071 |
| selectivity[M_all].y1 | 0.000 | 0.000 | -16.840 | 24.606 | 24.606 | 6.491 |
| selectivity[M_all].y2 | 0.000 | 0.000 | -0.741 | -12.665 | -12.665 | -5.249 |
| selectivity[summerTANSel_m].a50 | 0.000 | 0.000 | -2.881 | 3.430 | 3.430 | 0.868 |
| selectivity[summerTANSel_m].ato95 | 0.000 | 0.000 | -1.473 | 0.398 | 0.398 | 0.056 |
| selectivity[summerTANSel_m].alpha | 0.000 | 0.000 | 1.329 | -1.344 | -1.344 | -0.106 |
| selectivity[summerTANSel_f].a50 | 0.000 | 0.000 | -2.691 | 3.170 | 3.170 | 0.664 |
| selectivity[summerTANSel_f].ato95 | 0.000 | 0.000 | -0.490 | 0.595 | 0.595 | -0.480 |
| selectivity[autumnTANSel_m].a50 | 0.000 | 0.000 | -2.358 | -4.007 | -4.007 | 0.357 |
| selectivity[autumnTANSel_m].ato95 | 0.000 | 0.000 | 0.644 | -29.289 | -29.289 | -1.382 |
| selectivity[autumnTANSel_m].alpha | 0.000 | 0.000 | 0.906 | -1.965 | -1.965 | 0.644 |
| selectivity[autumnTANSel_f].a50 | 0.000 | 0.000 | -2.413 | -0.130 | -0.130 | 0.002 |
| selectivity[autumnTANSel_f].ato95 | 0.000 | 0.000 | 1.146 | -9.208 | -9.208 | -2.329 |
| selectivity[trwlFSel_m].mu | 0.000 | 0.000 | -0.397 | 3.926 | 3.926 | 0.592 |
| selectivity[trwlFSel_m].sigma_l | 0.000 | 0.000 | 1.161 | 7.106 | 7.106 | 0.378 |
| selectivity[trwlFSel_m].sigma_r | 0.000 | 0.000 | -225.082 | -181.401 | -181.401 | -218.291 |
| selectivity[trwlFSel_m].alpha | 0.000 | 0.000 | 2.101 | 0.980 | 0.980 | 1.121 |
| selectivity[trwlFSel_f].mu | 0.000 | 0.000 | -0.935 | 2.421 | 2.421 | 0.212 |
| selectivity[trwlFSel_f].sigma_l | 0.000 | 0.000 | 0.385 | 3.514 | 3.514 | -0.303 |
| selectivity[trwlFSel_f].sigma_r | 0.000 | 0.000 | 5.952 | -72.482 | -72.481 | -354.280 |
| selectivity[lineHomeFSel_m].a50 | 0.000 | 0.000 | 24.857 | 2.673 | 2.674 | 9.820 |
| selectivity[lineHomeFSel_m].ato95 | 0.000 | 0.000 | 46.606 | -0.062 | -0.062 | 14.389 |
| selectivity[lineHomeFSel_m].alpha | 0.000 | 0.000 | 29.007 | 4.900 | 4.900 | 12.971 |
| selectivity[lineHomeFSel_f].a50 | 0.000 | 0.000 | 0.845 | -0.457 | -0.457 | 0.018 |
| selectivity[lineHomeFSel_f].ato95 | 0.000 | 0.000 | 4.638 | -2.289 | -2.289 | -0.641 |
| selectivity[lineSpawnFSel_m].a50 | 0.000 | 0.000 | 22.884 | -57.587 | -57.587 | -64.466 |
| selectivity[lineSpawnFSel_m].ato95 | 0.000 | 0.000 | 26.276 | -44.948 | -44.948 | -49.741 |
| selectivity[lineSpawnFSel_m].alpha | 0.000 | 0.000 | 36.731 | -153.318 | -153.318 | -168.448 |
| selectivity[lineSpawnFSel_f].a50 | 0.000 | 0.000 | 0.245 | 0.073 | 0.073 | -0.848 |
| selectivity[lineSpawnFSel_f].ato95 | 0.000 | 0.000 | 3.246 | 1.499 | 1.499 | -3.851 |
| process[Recruitment].ycs_values{1972} | 0.000 | 0.000 | 3.589 | -98.618 | -98.618 | 2.792 |
| process[Recruitment].ycs_values{1973} | 0.000 | 0.000 | 2.389 | 63.078 | 63.078 | 2.557 |
| process[Recruitment].ycs_values{1974} | 0.000 | 0.000 | 0.675 | -135.483 | -135.485 | 2.995 |
| process[Recruitment].ycs_values{1975} | 0.000 | 0.000 | -0.064 | -87.331 | -87.331 | 0.659 |
| process[Recruitment].ycs_values{1976} | 0.000 | 0.000 | -0.916 | -34.578 | -34.578 | 1.599 |
| process[Recruitment].ycs_values{1977} | 0.000 | 0.000 | -2.353 | -101.420 | -101.420 | 0.004 |
| process[Recruitment].ycs_values{1978} | 0.000 | 0.000 | -2.733 | -56.206 | -56.206 | 0.346 |
| process[Recruitment].ycs_values{1979} | 0.000 | 0.000 | -3.185 | -82.743 | -82.743 | -0.835 |
| process[Recruitment].ycs_values{1980} | 0.000 | 0.000 | -2.457 | -57.547 | -57.547 | -0.239 |
| process[Recruitment].ycs_values{1981} | 0.000 | 0.000 | -1.962 | -76.622 | -76.622 | -0.649 |
| process[Recruitment].ycs_values{1982} | 0.000 | 0.000 | -0.906 | -75.037 | -75.038 | -0.152 |
| process[Recruitment].ycs_values{1983} | 0.000 | 0.000 | -1.056 | -74.210 | -74.210 | -1.353 |
| process[Recruitment].ycs_values{1984} | 0.000 | 0.000 | -0.115 | -65.490 | -65.490 | -0.883 |
| process[Recruitment].ycs_values{1985} | 0.000 | 0.000 | 0.162 | -74.561 | -74.561 | -1.313 |
| process[Recruitment].ycs_values{1986} | 0.000 | 0.000 | -0.236 | -85.692 | -85.692 | -1.545 |
| process[Recruitment].ycs_values{1987} | 0.000 | 0.000 | 0.091 | -83.683 | -83.683 | -0.925 |
| process[Recruitment].ycs_values{1988} | 0.000 | 0.000 | -0.079 | -59.635 | -59.635 | -1.290 |
| process[Recruitment].ycs_values{1989} | 0.000 | 0.000 | 0.884 | -76.381 | -76.381 | -0.775 |
| process[Recruitment].ycs_values{1990} | 0.000 | 0.000 | 0.106 | -83.808 | -83.808 | -1.256 |
| process[Recruitment].ycs_values{1991} | 0.000 | 0.000 | -0.436 | -69.043 | -69.043 | -0.539 |
| process[Recruitment].ycs_values{1992} | 0.000 | 0.000 | -0.325 | -79.442 | -79.442 | -0.772 |
| process[Recruitment].ycs_values{1993} | 0.000 | 0.000 | -0.871 | -71.947 | -71.947 | 0.307 |
| process[Recruitment].ycs_values{1994} | 0.000 | 0.000 | -0.102 | -72.582 | -72.582 | -0.285 |
| process[Recruitment].ycs_values{1995} | 0.000 | 0.000 | -0.691 | -61.908 | -61.908 | 0.373 |
| process[Recruitment].ycs_values{1996} | 0.000 | 0.000 | -0.736 | -66.552 | -66.552 | 0.074 |
| process[Recruitment].ycs_values{1997} | 0.000 | 0.000 | -0.400 | -68.176 | -68.176 | 0.416 |
| process[Recruitment].ycs_values{1998} | 0.000 | 0.000 | -0.368 | -70.707 | -70.708 | -0.144 |
| process[Recruitment].ycs_values{1999} | 0.000 | 0.000 | -0.045 | -76.243 | -76.243 | 0.366 |
| process[Recruitment].ycs_values{2000} | 0.000 | 0.000 | 0.239 | -63.330 | -63.330 | -0.122 |
| process[Recruitment].ycs_values{2001} | 0.000 | 0.000 | 0.623 | -64.995 | -64.995 | -0.075 |
| process[Recruitment].ycs_values{2002} | 0.000 | 0.000 | 0.227 | -72.280 | -72.280 | -0.424 |
| process[Recruitment].ycs_values{2003} | 0.000 | 0.000 | -0.008 | -64.376 | -64.376 | -0.226 |
| process[Recruitment].ycs_values{2004} | 0.000 | 0.000 | -0.260 | -67.157 | -67.157 | -0.985 |
| process[Recruitment].ycs_values{2005} | 0.000 | 0.000 | 0.321 | -62.817 | -62.817 | -0.618 |
| process[Recruitment].ycs_values{2006} | 0.000 | 0.000 | 0.123 | -69.327 | -69.327 | -0.865 |
| process[Recruitment].ycs_values{2007} | 0.000 | 0.000 | 0.042 | -54.491 | -54.491 | -0.760 |
| process[Recruitment].ycs_values{2008} | 0.000 | 0.000 | 0.503 | -61.176 | -61.176 | -0.738 |
| process[Recruitment].ycs_values{2009} | 0.000 | 0.000 | 1.010 | -48.629 | -48.629 | -0.072 |
| process[Recruitment].ycs_values{2010} | 0.000 | 0.000 | 0.674 | -51.171 | -51.171 | 0.464 |
| process[Recruitment].ycs_values{2011} | 0.000 | 0.000 | 1.004 | -79.526 | -79.526 | 0.088 |
| process[Recruitment].ycs_values{2012} | 0.000 | 0.000 | -0.311 | -62.893 | -62.893 | -0.086 |
| process[Recruitment].ycs_values{2013} | 0.000 | 0.000 | 1.918 | -60.698 | -60.698 | -0.555 |
| process[Recruitment].ycs_values{2014} | 0.000 | 0.000 | 0.262 | -67.785 | -67.785 | -0.626 |
| Component | Base_Model | Sensitivity_1 |
|---|---|---|
| Tangaroa_bio_autumn | -6.829 | -6.834 |
| Tangaroa_bio_summer | -23.880 | -23.960 |
| Tangaroa_propn_at_age_aut | 175.700 | 175.800 |
| Tangaroa_propn_at_age_summer | 835.900 | 835.600 |
| longline_Campbell_home_propn_at_age | 275.700 | 275.400 |
| longline_Puysegur_spawn_propn_at_age | 363.300 | 363.300 |
| trawl_observer_propn_at_age | 682.600 | 682.300 |
| prior_on_q[tan_sum].q | -2.364 | -2.366 |
| prior_on_q[tan_aut].q | -2.033 | -2.037 |
| prior_on_initialization.B0 | 12.640 | 12.650 |
| prior_on_natural_mortality.ogive_all | 0.000 | 0.000 |
| prior_on_selectivity[surveysum_sel].male | 0.000 | 0.000 |
| prior_on_selectivity[surveysum_sel].female | 0.000 | 0.000 |
| prior_on_selectivity[surveyaut_sel].male | 0.000 | 0.000 |
| prior_on_selectivity[surveyaut_sel].female | 0.000 | 0.000 |
| prior_on_selectivity[trawl_sel].male | 0.000 | 0.000 |
| prior_on_selectivity[trawl_sel].female | 0.000 | 0.000 |
| prior_on_selectivity[line_home_sel].male | 0.000 | 0.000 |
| prior_on_selectivity[line_home_sel].female | 0.000 | 0.000 |
| prior_on_selectivity[line_spawn_sel].male | 0.000 | 0.000 |
| prior_on_selectivity[line_spawn_sel].female | 0.000 | 0.000 |
| prior_on_recruitment.YCS | -14.440 | -14.370 |
| clp1 | 0.000 | 0.000 |
| clp2 | 0.000 | 0.000 |
| clp3 | 0.000 | 0.000 |
| YCS_average_1 | 0.908 | 0.904 |
| Total | 2297.000 | 2296.000 |
| rownames | betadiff_casal_flags_on | betadiff_casal_flags_off | betadiff_casal_flags_on_low_tol | adolc_casal_flags_on | adolc_casal_flags_off | adolc_casal_flags_on_low_tol |
|---|---|---|---|---|---|---|
| observation->summerTANbiomass-1992 | -1.693 | -1.693 | -1.679 | -1.631 | -1.631 | -1.678 |
| observation->summerTANbiomass-1993 | -1.353 | -1.353 | -1.331 | -1.221 | -1.221 | -1.318 |
| observation->summerTANbiomass-1994 | -0.975 | -0.975 | -0.991 | -1.091 | -1.091 | -1.012 |
| observation->summerTANbiomass-2001 | 0.430 | 0.430 | 0.354 | 0.273 | 0.273 | 0.411 |
| observation->summerTANbiomass-2002 | -1.778 | -1.778 | -1.786 | -1.787 | -1.787 | -1.778 |
| observation->summerTANbiomass-2003 | -1.685 | -1.685 | -1.693 | -1.688 | -1.688 | -1.683 |
| observation->summerTANbiomass-2004 | -1.598 | -1.598 | -1.586 | -1.600 | -1.600 | -1.604 |
| observation->summerTANbiomass-2005 | -1.657 | -1.657 | -1.656 | -1.658 | -1.658 | -1.658 |
| observation->summerTANbiomass-2006 | -1.143 | -1.143 | -1.153 | -1.179 | -1.179 | -1.165 |
| observation->summerTANbiomass-2007 | -1.162 | -1.162 | -1.180 | -1.211 | -1.211 | -1.182 |
| observation->summerTANbiomass-2008 | -1.568 | -1.568 | -1.553 | -1.513 | -1.513 | -1.553 |
| observation->summerTANbiomass-2009 | -1.700 | -1.700 | -1.705 | -1.715 | -1.715 | -1.704 |
| observation->summerTANbiomass-2010 | -1.672 | -1.672 | -1.678 | -1.698 | -1.698 | -1.675 |
| observation->summerTANbiomass-2012 | -1.554 | -1.554 | -1.558 | -1.596 | -1.596 | -1.552 |
| observation->summerTANbiomass-2013 | -1.669 | -1.669 | -1.667 | -1.634 | -1.634 | -1.671 |
| observation->summerTANbiomass-2015 | -1.582 | -1.582 | -1.570 | -1.416 | -1.416 | -1.591 |
| observation->summerTANbiomass-2017 | -1.526 | -1.526 | -1.528 | -1.517 | -1.517 | -1.526 |
| observation->Tangaroa_propn_at_age_summer-1990 | 44.218 | 44.218 | 44.393 | 44.200 | 44.200 | 44.252 |
| observation->Tangaroa_propn_at_age_summer-1992 | 51.993 | 51.993 | 51.753 | 52.283 | 52.283 | 52.033 |
| observation->Tangaroa_propn_at_age_summer-1993 | 50.200 | 50.200 | 50.168 | 50.265 | 50.265 | 50.218 |
| observation->Tangaroa_propn_at_age_summer-1994 | 49.743 | 49.743 | 49.785 | 49.782 | 49.782 | 49.708 |
| observation->Tangaroa_propn_at_age_summer-2001 | 48.355 | 48.355 | 48.237 | 48.568 | 48.568 | 48.471 |
| observation->Tangaroa_propn_at_age_summer-2002 | 47.830 | 47.830 | 47.879 | 48.038 | 48.038 | 47.817 |
| observation->Tangaroa_propn_at_age_summer-2003 | 48.442 | 48.442 | 48.620 | 48.412 | 48.412 | 48.392 |
| observation->Tangaroa_propn_at_age_summer-2004 | 44.823 | 44.823 | 44.865 | 44.903 | 44.903 | 44.825 |
| observation->Tangaroa_propn_at_age_summer-2005 | 43.097 | 43.097 | 43.117 | 43.060 | 43.060 | 43.126 |
| observation->Tangaroa_propn_at_age_summer-2006 | 43.891 | 43.891 | 44.058 | 43.942 | 43.942 | 43.859 |
| observation->Tangaroa_propn_at_age_summer-2007 | 41.848 | 41.848 | 41.841 | 41.824 | 41.824 | 41.858 |
| observation->Tangaroa_propn_at_age_summer-2008 | 45.225 | 45.225 | 45.267 | 45.127 | 45.127 | 45.217 |
| observation->Tangaroa_propn_at_age_summer-2009 | 46.844 | 46.844 | 46.806 | 46.994 | 46.994 | 46.806 |
| observation->Tangaroa_propn_at_age_summer-2010 | 47.128 | 47.128 | 47.202 | 47.196 | 47.196 | 47.192 |
| observation->Tangaroa_propn_at_age_summer-2012 | 44.353 | 44.353 | 44.183 | 44.772 | 44.772 | 44.409 |
| observation->Tangaroa_propn_at_age_summer-2013 | 47.251 | 47.251 | 47.021 | 47.416 | 47.416 | 47.262 |
| observation->Tangaroa_propn_at_age_summer-2015 | 46.473 | 46.473 | 46.342 | 46.718 | 46.718 | 46.475 |
| observation->Tangaroa_propn_at_age_summer-2017 | 44.182 | 44.182 | 44.082 | 44.204 | 44.204 | 44.191 |
| observation->autumnTANbiomass-1992 | -1.558 | -1.558 | -1.572 | -1.570 | -1.570 | -1.559 |
| observation->autumnTANbiomass-1993 | -1.741 | -1.741 | -1.733 | -1.726 | -1.726 | -1.738 |
| observation->autumnTANbiomass-1996 | -1.779 | -1.779 | -1.779 | -1.778 | -1.778 | -1.778 |
| observation->autumnTANbiomass-1998 | -1.750 | -1.750 | -1.750 | -1.750 | -1.750 | -1.750 |
| observation->Tangaroa_propn_at_age_autumn-1992 | 44.589 | 44.589 | 44.443 | 44.805 | 44.805 | 44.577 |
| observation->Tangaroa_propn_at_age_autumn-1993 | 45.484 | 45.484 | 45.443 | 45.684 | 45.684 | 45.494 |
| observation->Tangaroa_propn_at_age_autumn-1996 | 42.184 | 42.184 | 42.295 | 42.483 | 42.483 | 42.185 |
| observation->Tangaroa_propn_at_age_autumn-1998 | 43.464 | 43.464 | 43.610 | 43.225 | 43.225 | 43.468 |
| observation->trawl_propn_at_age-1992 | 36.067 | 36.067 | 35.944 | 36.594 | 36.594 | 36.013 |
| observation->trawl_propn_at_age-1993 | 27.516 | 27.516 | 27.476 | 27.571 | 27.571 | 27.512 |
| observation->trawl_propn_at_age-1994 | 25.819 | 25.819 | 25.764 | 25.964 | 25.964 | 25.768 |
| observation->trawl_propn_at_age-1996 | 28.394 | 28.394 | 28.397 | 28.617 | 28.617 | 28.441 |
| observation->trawl_propn_at_age-1998 | 24.915 | 24.915 | 24.910 | 25.032 | 25.032 | 24.920 |
| observation->trawl_propn_at_age-2001 | 24.580 | 24.580 | 24.542 | 24.685 | 24.685 | 24.563 |
| observation->trawl_propn_at_age-2002 | 26.770 | 26.770 | 26.792 | 26.936 | 26.936 | 26.779 |
| observation->trawl_propn_at_age-2003 | 34.564 | 34.564 | 34.511 | 34.570 | 34.570 | 34.586 |
| observation->trawl_propn_at_age-2004 | 29.608 | 29.608 | 29.608 | 29.604 | 29.604 | 29.505 |
| observation->trawl_propn_at_age-2005 | 30.147 | 30.147 | 30.166 | 30.267 | 30.267 | 30.125 |
| observation->trawl_propn_at_age-2006 | 33.629 | 33.629 | 33.714 | 33.729 | 33.729 | 33.593 |
| observation->trawl_propn_at_age-2007 | 26.635 | 26.635 | 26.588 | 26.662 | 26.662 | 26.617 |
| observation->trawl_propn_at_age-2008 | 27.059 | 27.059 | 27.076 | 27.053 | 27.053 | 27.077 |
| observation->trawl_propn_at_age-2009 | 37.213 | 37.213 | 37.237 | 37.210 | 37.210 | 37.217 |
| observation->trawl_propn_at_age-2010 | 30.648 | 30.648 | 30.694 | 30.594 | 30.594 | 30.722 |
| observation->trawl_propn_at_age-2011 | 31.266 | 31.266 | 31.260 | 31.339 | 31.339 | 31.245 |
| observation->trawl_propn_at_age-2012 | 32.325 | 32.325 | 32.366 | 32.237 | 32.237 | 32.363 |
| observation->trawl_propn_at_age-2013 | 37.072 | 37.072 | 36.943 | 36.843 | 36.843 | 36.957 |
| observation->trawl_propn_at_age-2014 | 30.640 | 30.640 | 30.642 | 30.576 | 30.576 | 30.632 |
| observation->trawl_propn_at_age-2015 | 33.456 | 33.456 | 33.474 | 33.327 | 33.327 | 33.491 |
| observation->trawl_propn_at_age-2016 | 36.532 | 36.532 | 36.482 | 36.368 | 36.368 | 36.534 |
| observation->trawl_propn_at_age-2017 | 37.755 | 37.755 | 37.708 | 37.641 | 37.641 | 37.795 |
| observation->longline_Campbell_home_propn_at_age-1999 | 45.348 | 45.348 | 45.256 | 45.143 | 45.143 | 45.309 |
| observation->longline_Campbell_home_propn_at_age-2001 | 31.965 | 31.965 | 31.950 | 31.934 | 31.934 | 31.984 |
| observation->longline_Campbell_home_propn_at_age-2003 | 28.644 | 28.644 | 28.675 | 28.610 | 28.610 | 28.677 |
| observation->longline_Campbell_home_propn_at_age-2005 | 32.750 | 32.750 | 32.776 | 32.826 | 32.826 | 32.749 |
| observation->longline_Campbell_home_propn_at_age-2009 | 26.033 | 26.033 | 25.611 | 25.886 | 25.886 | 25.939 |
| observation->longline_Campbell_home_propn_at_age-2010 | 24.302 | 24.302 | 24.461 | 24.338 | 24.338 | 24.326 |
| observation->longline_Campbell_home_propn_at_age-2011 | 28.878 | 28.878 | 28.935 | 28.747 | 28.747 | 28.882 |
| observation->longline_Campbell_home_propn_at_age-2012 | 32.258 | 32.258 | 32.389 | 32.249 | 32.249 | 32.279 |
| observation->longline_Campbell_home_propn_at_age-2014 | 25.495 | 25.495 | 25.357 | 25.391 | 25.391 | 25.451 |
| observation->longline_Puyseger_home_propn_at_age-2000 | 42.745 | 42.745 | 42.680 | 42.956 | 42.956 | 43.129 |
| observation->longline_Puyseger_home_propn_at_age-2001 | 31.770 | 31.770 | 31.900 | 31.791 | 31.791 | 31.977 |
| observation->longline_Puyseger_home_propn_at_age-2002 | 39.978 | 39.978 | 39.998 | 40.179 | 40.179 | 40.361 |
| observation->longline_Puyseger_home_propn_at_age-2003 | 43.527 | 43.527 | 43.511 | 43.694 | 43.694 | 43.560 |
| observation->longline_Puyseger_home_propn_at_age-2004 | 39.957 | 39.957 | 40.015 | 40.076 | 40.076 | 40.140 |
| observation->longline_Puyseger_home_propn_at_age-2005 | 25.532 | 25.532 | 25.358 | 25.506 | 25.506 | 25.482 |
| observation->longline_Puyseger_home_propn_at_age-2006 | 35.210 | 35.210 | 35.426 | 35.107 | 35.107 | 35.010 |
| observation->longline_Puyseger_home_propn_at_age-2007 | 33.981 | 33.981 | 33.782 | 34.137 | 34.137 | 34.361 |
| observation->longline_Puyseger_home_propn_at_age-2008 | 19.139 | 19.139 | 19.113 | 19.090 | 19.090 | 19.135 |
| observation->longline_Puyseger_home_propn_at_age-2010 | 24.238 | 24.238 | 24.366 | 24.038 | 24.038 | 23.920 |
| observation->longline_Puyseger_home_propn_at_age-2017 | 27.200 | 27.200 | 27.093 | 27.441 | 27.441 | 27.656 |
| prior->B0->process[Recruitment].b0 | 12.640 | 12.640 | 12.646 | 12.492 | 12.492 | 12.587 |
| prior->summerTANq->catchability[summerTANq].q | -2.363 | -2.363 | -2.365 | -2.240 | -2.240 | -2.318 |
| prior->autumnTANq->catchability[autumnTANq].q | -2.035 | -2.035 | -2.037 | -1.786 | -1.786 | -1.939 |
| prior->M_all_x0->selectivity[M_all].x0 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->M_all_y0->selectivity[M_all].y0 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->M_all_y1->selectivity[M_all].y1 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->M_all_y2->selectivity[M_all].y2 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[summerTANSel_m].a50 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[summerTANSel_m].ato95 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[summerTANSel_m].alpha | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[summerTANSel_f].a50 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[summerTANSel_f].ato95 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[autumnTANSel_m].a50 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[autumnTANSel_m].ato95 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[autumnTANSel_m].alpha | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[autumnTANSel_f].a50 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[autumnTANSel_f].ato95 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[trwlFSel_m].mu | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[trwlFSel_m].sigma_l | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[trwlFSel_m].sigma_r | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[trwlFSel_m].alpha | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[trwlFSel_f].mu | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[trwlFSel_f].sigma_l | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[trwlFSel_f].sigma_r | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[lineHomeFSel_m].a50 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[lineHomeFSel_m].ato95 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[lineHomeFSel_m].alpha | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[lineHomeFSel_f].a50 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[lineHomeFSel_f].ato95 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[lineSpawnFSel_m].a50 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[lineSpawnFSel_m].ato95 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[lineSpawnFSel_m].alpha | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[lineSpawnFSel_f].a50 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->selectivity[lineSpawnFSel_f].ato95 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->process[Recruitment].ycs_values{1972} | -0.378 | -0.378 | -0.365 | -0.008 | -0.008 | -0.368 |
| prior->process[Recruitment].ycs_values{1973} | -0.360 | -0.360 | -0.349 | 1.324 | 1.324 | -0.348 |
| prior->process[Recruitment].ycs_values{1974} | -0.397 | -0.397 | -0.398 | 0.594 | 0.594 | -0.399 |
| prior->process[Recruitment].ycs_values{1975} | -0.398 | -0.398 | -0.398 | 0.143 | 0.143 | -0.398 |
| prior->process[Recruitment].ycs_values{1976} | -0.380 | -0.380 | -0.383 | -0.361 | -0.361 | -0.375 |
| prior->process[Recruitment].ycs_values{1977} | -0.399 | -0.399 | -0.398 | 0.230 | 0.230 | -0.399 |
| prior->process[Recruitment].ycs_values{1978} | -0.398 | -0.398 | -0.396 | -0.122 | -0.122 | -0.398 |
| prior->process[Recruitment].ycs_values{1979} | -0.335 | -0.335 | -0.316 | 0.462 | 0.462 | -0.330 |
| prior->process[Recruitment].ycs_values{1980} | -0.380 | -0.380 | -0.372 | 0.017 | 0.017 | -0.379 |
| prior->process[Recruitment].ycs_values{1981} | -0.231 | -0.231 | -0.213 | 0.696 | 0.696 | -0.225 |
| prior->process[Recruitment].ycs_values{1982} | -0.364 | -0.364 | -0.367 | -0.206 | -0.206 | -0.364 |
| prior->process[Recruitment].ycs_values{1983} | -0.326 | -0.326 | -0.319 | 0.396 | 0.396 | -0.318 |
| prior->process[Recruitment].ycs_values{1984} | -0.291 | -0.291 | -0.292 | -0.343 | -0.343 | -0.297 |
| prior->process[Recruitment].ycs_values{1985} | -0.394 | -0.394 | -0.393 | -0.095 | -0.095 | -0.395 |
| prior->process[Recruitment].ycs_values{1986} | -0.114 | -0.114 | -0.117 | -0.373 | -0.373 | -0.132 |
| prior->process[Recruitment].ycs_values{1987} | -0.135 | -0.135 | -0.134 | -0.371 | -0.371 | -0.146 |
| prior->process[Recruitment].ycs_values{1988} | -0.334 | -0.334 | -0.334 | -0.326 | -0.326 | -0.341 |
| prior->process[Recruitment].ycs_values{1989} | -0.375 | -0.375 | -0.372 | -0.167 | -0.167 | -0.378 |
| prior->process[Recruitment].ycs_values{1990} | -0.350 | -0.350 | -0.350 | -0.186 | -0.186 | -0.356 |
| prior->process[Recruitment].ycs_values{1991} | -0.384 | -0.384 | -0.385 | -0.183 | -0.183 | -0.385 |
| prior->process[Recruitment].ycs_values{1992} | -0.367 | -0.367 | -0.369 | -0.171 | -0.171 | -0.370 |
| prior->process[Recruitment].ycs_values{1993} | -0.225 | -0.225 | -0.217 | 0.650 | 0.650 | -0.228 |
| prior->process[Recruitment].ycs_values{1994} | -0.233 | -0.233 | -0.232 | 0.639 | 0.639 | -0.230 |
| prior->process[Recruitment].ycs_values{1995} | -0.192 | -0.192 | -0.185 | 0.590 | 0.590 | -0.196 |
| prior->process[Recruitment].ycs_values{1996} | -0.319 | -0.319 | -0.315 | 0.329 | 0.329 | -0.320 |
| prior->process[Recruitment].ycs_values{1997} | -0.399 | -0.399 | -0.399 | -0.055 | -0.055 | -0.399 |
| prior->process[Recruitment].ycs_values{1998} | -0.372 | -0.372 | -0.373 | -0.209 | -0.209 | -0.373 |
| prior->process[Recruitment].ycs_values{1999} | -0.360 | -0.360 | -0.360 | -0.207 | -0.207 | -0.358 |
| prior->process[Recruitment].ycs_values{2000} | -0.399 | -0.399 | -0.399 | -0.084 | -0.084 | -0.399 |
| prior->process[Recruitment].ycs_values{2001} | -0.399 | -0.399 | -0.399 | -0.094 | -0.094 | -0.399 |
| prior->process[Recruitment].ycs_values{2002} | -0.378 | -0.378 | -0.377 | -0.182 | -0.182 | -0.380 |
| prior->process[Recruitment].ycs_values{2003} | -0.399 | -0.399 | -0.399 | -0.089 | -0.089 | -0.399 |
| prior->process[Recruitment].ycs_values{2004} | -0.383 | -0.383 | -0.383 | 0.090 | 0.090 | -0.381 |
| prior->process[Recruitment].ycs_values{2005} | -0.249 | -0.249 | -0.251 | 0.472 | 0.472 | -0.243 |
| prior->process[Recruitment].ycs_values{2006} | -0.375 | -0.375 | -0.375 | 0.155 | 0.155 | -0.372 |
| prior->process[Recruitment].ycs_values{2007} | -0.252 | -0.252 | -0.253 | 0.358 | 0.358 | -0.246 |
| prior->process[Recruitment].ycs_values{2008} | -0.368 | -0.368 | -0.370 | 0.104 | 0.104 | -0.365 |
| prior->process[Recruitment].ycs_values{2009} | -0.320 | -0.320 | -0.326 | 0.126 | 0.126 | -0.320 |
| prior->process[Recruitment].ycs_values{2010} | -0.362 | -0.362 | -0.364 | 0.031 | 0.031 | -0.364 |
| prior->process[Recruitment].ycs_values{2011} | -0.392 | -0.392 | -0.390 | -0.069 | -0.069 | -0.392 |
| prior->process[Recruitment].ycs_values{2012} | -0.394 | -0.394 | -0.393 | -0.018 | -0.018 | -0.394 |
| prior->process[Recruitment].ycs_values{2013} | -0.389 | -0.389 | -0.393 | -0.002 | -0.002 | -0.388 |
| prior->process[Recruitment].ycs_values{2014} | -0.396 | -0.396 | -0.396 | 0.000 | 0.000 | -0.395 |
| additional_prior->YCS_average_1 | 0.908 | 0.908 | 0.904 | 0.006 | 0.006 | 0.905 |
| total_negloglike | 2296.970 | 2296.970 | 2296.140 | 2317.710 | 2317.710 | 2298.450 |
| total_score | 2296.970 | 2296.970 | 2296.140 | 2317.710 | 2317.710 | 2298.450 |
## [1] "CASAL base model convergence information"
## [1] "fmm: have converged: t = 0.00198541 f = 2297.19"
## [2] "Successful convergence in optimise"
## [3] "Minimiser achieved convergence after 53 quasi-Newton iterations using 91 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-006"
## [2] "fmm: have converged: t = 4.30035e-007 f = 2296.34"
## [3] "Successful convergence in optimise"
## [4] "Minimiser achieved convergence after 188 quasi-Newton iterations using 303 objective function evaluations"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: have converged: t = 4.70876e-07 f = 2296.14"
## [2] "Successful convergence in optimise"
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## [1] "[IMPORTANT] FMM: Small step size convergence"
## [2] "FMM: Small step size convergence"
## [1] "CASAL model warnings"
## NULL
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
## parameter estimate lower.bound upper.bound
## 1 selectivity[trawl_sel].male[3] 200 1 200
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## [2] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## [1] ""
Time series comparisons with CASAL base model results
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
Derived quantities
SB0, SBcurrent, MSY, F_MSY, others…
Comparison plots
## [1] "CASAL base parameter correlation range (excluding 1.0): -0.7359 0.9329"
## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.9871 0.9823"
## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"
## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"
## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"
## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"
## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"
## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"